Arthur Rand

Hello @rugilemat, Is it possible that you have an older version in your `PATH` and it's taking precedence over the version you've downloaded? I just downloaded the [latest release](https://github.com/nanoporetech/modkit/releases/tag/v0.3.1) and:...

@rugilemat any luck?

Hello @lkwhite, Could you run `modkit extract` with `--log-filepath $log_file` and attach it? It should tell you why reads are failing.

Hello @lkwhite, It is possible that remora reference anchoring doesn't emit the correct MN tag or doesn't update it when the sequence length changes. Could you try removing the MN...

Hello @lkwhite, The MN tag isn't in the spec [yet](https://github.com/samtools/hts-specs/pull/714), and remora doesn't use it. But dorado does, so we need to update the recommendation to remove the tags when...

Just in case anyone else encounters an issue with large number of skipped or error reads following "reference-anchored" remora base modification calling. If you have previously used base modification calling...

Hello @Proy321, The score and MAP-based p-value are calculated using the `sample a` and `sample b` counts (columns 6 and 8, respectively). In the case of the MAP-based p-value, counts...

Hello @Proy321, > Is there a way to incorporate multiple samples in the -a and -b options in --segment option . Yes, as [documented](https://nanoporetech.github.io/modkit/intro_dmr.html#3-detecting-differential-modification-at-single-base-positions), use can pass `-a` and `-b`...

Hello @Proy321, To answer your [first question](https://github.com/nanoporetech/modkit/issues/191#issuecomment-2139311278) regarding the interpretation of the DMR output. Both positions (8441 and 8443) are the same. In sample `a` there are 3 reads at...

Hello @PRIYANKA-22091995, If you have a site with 0 of 5 reads reporting modification (all 5 report canonical) in one condition and 7 of 7 reporting methylation (of any type)...